Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.517 kcal/mol/HA)
✓ Good fit quality (FQ -5.13)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (38.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-17.064
kcal/mol
LE
-0.517
kcal/mol/HA
Fit Quality
-5.13
FQ (Leeson)
HAC
33
heavy atoms
MW
467
Da
LogP
2.20
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 38.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 1
Clashes 11
Severe clashes 0
| Final rank | 8.047603473549973 | Score | -17.0635 |
|---|---|---|---|
| Inter norm | -0.650302 | Intra norm | 0.133228 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 11 protein contact clashes; high strain Δ 54.1 | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:THR54;A:TRP47;A:VAL156;A:VAL49 | ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 11 | Native recall | 0.55 |
| Jaccard | 0.44 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 457 | 6.227235650424467 | -0.869908 | -25.3855 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 499 | 7.924145885427372 | -0.811154 | -25.1852 | 1 | 21 | 18 | 0.90 | 0.20 | - | no | Open |
| 500 | 8.047603473549973 | -0.650302 | -17.0635 | 4 | 16 | 11 | 0.55 | 0.20 | - | no | Current |
| 502 | 7.886561522190485 | -0.671567 | -20.5051 | 0 | 19 | 17 | 0.85 | 0.00 | - | yes | Open |
| 458 | 9.071259306486594 | -0.892016 | -21.1864 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 498 | 10.948540452705352 | -0.672343 | -13.0016 | 3 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 501 | 11.089205202628005 | -0.806644 | -22.0054 | 3 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 497 | 11.339105867695721 | -0.802805 | -23.1126 | 3 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.064kcal/mol
Ligand efficiency (LE)
-0.5171kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.130
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
466.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.20
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.80kcal/mol
Minimised FF energy
2.93kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.